Purpose: derive metrics of fragmentation and connectivity for reporting units

8.0.1 Load spatial data

Code
# basin
basin <- vect("/Users/jeffbaldock/Library/CloudStorage/GoogleDrive-jbaldock@uwyo.edu/Shared drives/wyo-coop-baldock/UWyoming/Snake River Cutthroat/Data/Spatial/Basin Delineation/BasinDelineation/MajorBasins_Watersheds.shp") 
basin <- subset(basin, basin$site %in% c("SnakeHeadwaters"))

# reporting unit watersheds
watersheds <- vect("/Users/jeffbaldock/Library/CloudStorage/GoogleDrive-jbaldock@uwyo.edu/Shared drives/wyo-coop-baldock/UWyoming/Snake River Cutthroat/Analyses/Snake River GSI Quarto/Landscape Covariates/Watershed Delineation/RepUnits_Watersheds.shp")

# waterfalls
# falls <- terra::vect("/Users/jeffbaldock/Library/CloudStorage/GoogleDrive-jbaldock@uwyo.edu/Shared drives/wyo-coop-baldock/UWyoming/Snake River Cutthroat/Analyses/Snake River GSI Quarto/Landscape Covariates/Barriers/SARP Waterfalls/Archive_Falls_Mar082024.gdb")
# falls <- project(falls, crs(basin))
# falls <- crop(falls, basin)
# writeVector(falls, "/Users/jeffbaldock/Library/CloudStorage/GoogleDrive-jbaldock@uwyo.edu/Shared drives/wyo-coop-baldock/UWyoming/Snake River Cutthroat/Analyses/Snake River GSI Quarto/Landscape Covariates/Barriers/SARP Waterfalls/SARP_Waterfalls_SnakeHeadwaters.shp")
falls <- vect("/Users/jeffbaldock/Library/CloudStorage/GoogleDrive-jbaldock@uwyo.edu/Shared drives/wyo-coop-baldock/UWyoming/Snake River Cutthroat/Analyses/Snake River GSI Quarto/Landscape Covariates/Barriers/SARP Waterfalls/SARP_Waterfalls_SnakeHeadwaters.shp")
falls$BarrierType <- "Waterfall"

mapview(st_as_sf(falls))
Code
# barriers
barriers <- read_csv("/Users/jeffbaldock/Library/CloudStorage/GoogleDrive-jbaldock@uwyo.edu/Shared drives/wyo-coop-baldock/UWyoming/Snake River Cutthroat/Analyses/Snake River GSI Quarto/Landscape Covariates/Barriers/aquatic_barrier_ranks_Jan2025/aquatic_barrier_ranks.csv") %>% filter(Removed == "no", Passability %in% c("Complete barrier", "Partial passability", "Seasonably passable - non salmonid", "Seasonably passable - salmonid"), HasNetwork == "yes")
barriers <- vect(barriers, geom = c("lon", "lat"), crs = "+proj=longlat +datum=WGS84")
barriers <- project(barriers, crs(basin))

# combine falls and barriers
barriers_comb <- union(falls, barriers)
barriers_comb$BarrierType <- recode(barriers_comb$BarrierType, "Assessed road-related barrier" = "Road")

# map it
mapview(st_as_sf(watersheds)) + mapview(st_as_sf(barriers_comb), zcol = "BarrierType")

8.0.2 Fragmentation

Derive metric of habitat fragmentation as the number of barriers per square kilometer of watershed area.

Code
cell_counts <- terra::extract(watersheds, barriers_comb)
point_counts <- cell_counts %>% group_by(site) %>% summarise(numbarr = n()) %>% rename(repunit = site)

sitetib <- tibble(repunit = watersheds$site, areasqkm = watersheds$aresqkm) %>% left_join(point_counts) %>% replace_na(list(numbarr = 0)) %>% mutate(barrier_dens = numbarr/areasqkm)
write_csv(sitetib, "/Users/jeffbaldock/Library/CloudStorage/GoogleDrive-jbaldock@uwyo.edu/Shared drives/wyo-coop-baldock/UWyoming/Snake River Cutthroat/Analyses/Snake River GSI Quarto/Landscape Covariates/Barriers/RepUnits_BarrierSummary.csv")

8.0.3 Connectivity

Define binary variable describing connectivity between downstream extent of reporting unit and mainstem Snake River: 1 = connected and 0 = disconnected. Connectivity may be interrupted by barriers (as mapped above; e.g., waterfalls, culverts, or diversion dams) or by low flow/intermittent reaches (based on field observations/expert opinion…e.g., Spread, Ditch, etc.). Note: all streams in the Gros Ventre River and Spread Creek basins have connectivity = 0 because the lower Gros Vente River (between Hwy 191 and Spring Gulch Road) and lower Spread Creek () is intermittent during typical

Code
sitetib$connectivity <- c(1,1,1,1,1,1,0,1,1,1,1,0,1,1,0,0,1,1,1,0,1,0,1,0,1,1,0,1,1,0,1,0,0,1,1,1,1,1,1,1,1,0,1,1,1,1,0,1,1,1,1,1)
sitetib$connect_type <- c(NA,NA,NA,NA,NA,NA,"low flow",NA,NA,NA,NA,"low flow",NA,NA,"low flow","waterfall",NA,NA,NA,"low flow",NA,"waterfall",NA,"low flow",NA,NA,"low flow",NA,NA,"low flow",NA,"culvert","diversion dam",NA,NA,NA,NA,NA,NA,NA,NA,"waterfall",NA,NA,NA,NA,"culvert",NA,NA,NA,NA,NA)

8.0.4 Final data

Code
sitetib %>% kable()
repunit areasqkm numbarr barrier_dens connectivity connect_type
bailey_NA 41.5714362 0 0.0000000 1 NA
blackrock_lower 124.9215920 3 0.0240151 1 NA
blackrock_upper 80.6862046 2 0.0247874 1 NA
blacktail_NA 61.1445506 0 0.0000000 1 NA
blindbull_NA 36.3517449 3 0.0825270 1 NA
boulder_NA 53.6999801 0 0.0000000 1 NA
box_NA 29.1414701 0 0.0000000 0 low flow
cabin_NA 23.5100427 0 0.0000000 1 NA
clear_NA 16.6041016 0 0.0000000 1 NA
cliff_NA 158.3813174 9 0.0568249 1 NA
cody_bluecrane 18.5117071 0 0.0000000 1 NA
cottonwood_grosventre 89.1780292 2 0.0224270 0 low flow
cottonwood_nps 187.1527021 14 0.0748052 1 NA
cowboycabin_NA 6.6392953 0 0.0000000 1 NA
crystal_lower 185.1148874 0 0.0000000 0 low flow
crystal_upper 155.6115004 0 0.0000000 0 waterfall
deadman_greys 42.6069634 6 0.1408221 1 NA
deadmansbar_NA 11.7612083 0 0.0000000 1 NA
dell_NA 118.1568591 1 0.0084633 1 NA
ditch_NA 67.6914863 1 0.0147729 0 low flow
dog_NA 31.0904837 1 0.0321642 1 NA
fall_coburn 116.5315084 1 0.0085814 0 waterfall
fish_NA 233.3741441 7 0.0299948 1 NA
fish_grosventre 587.8758585 8 0.0136083 0 low flow
flat_NA 173.3686411 0 0.0000000 1 NA
fordspring_NA 0.3712985 0 0.0000000 1 NA
goosewing_NA 40.3960756 0 0.0000000 0 low flow
granite_lower 220.3826608 3 0.0136127 1 NA
granite_upper 131.1747886 3 0.0228702 1 NA
grosventre_lower 1589.6465468 28 0.0176140 0 low flow
hoback_upper 114.0778330 4 0.0350638 1 NA
horse_NA 63.2035547 2 0.0316438 0 culvert
lava_NA 65.3337290 0 0.0000000 0 diversion dam
leidy_NA 10.7360331 0 0.0000000 1 NA
littlegreys_steer 179.3457294 3 0.0167275 1 NA
lowerbarbc_NA 6.3968311 0 0.0000000 1 NA
mosquito_NA 61.6412867 4 0.0648916 1 NA
northbuffalofork_NA 211.7277107 8 0.0377844 1 NA
pacific_NA 415.0574929 8 0.0192744 1 NA
rock_NA 11.9857990 0 0.0000000 1 NA
shoal_NA 82.6496949 1 0.0120993 1 NA
slate_NA 97.2568238 1 0.0102821 0 waterfall
snakeriversidechannel_NA 18.8103796 0 0.0000000 1 NA
spread_southfork 98.9032021 1 0.0101109 1 NA
spread_uppermainstem 202.6088599 5 0.0246781 1 NA
spreadnf_flagstaff 62.1057535 3 0.0483047 1 NA
spring_nps 4.0130319 0 0.0000000 0 culvert
spring_tss 24.8578294 0 0.0000000 1 NA
threechannel_NA 32.3647548 0 0.0000000 1 NA
upperbarbc_NA 5.7370505 0 0.0000000 1 NA
white_NA 32.6721618 2 0.0612142 1 NA
willow_NA 185.7033361 2 0.0107699 1 NA